pullblast.py - retrieve BLAST HSP database hits in FASTA format, returning results in same strand orientation as query

pullblast.py

#Usage:
#blastall -p blastn -d db -i query -m 8 | python pullblast.py db.fasta

import sys
from Bio import SeqIO

records = SeqIO.to_dict(SeqIO.parse(open(sys.argv[1]), "fasta"))

for ln in sys.stdin:
        cols = ln.rstrip().split("\t")
        contig = cols[1]
        coord_start = int(cols[8])
        coord_end = int(cols[9])

        if coord_start > coord_end:
                coord_start, coord_end = coord_end, coord_start
                seq = records[contig][coord_start - 1:coord_end].reverse_complement(id=True, description=True)
        else:
                seq = records[contig][coord_start - 1:coord_end]

        SeqIO.write([seq], sys.stdout, "fasta")